Volume 131, Issue 5, Pages 915-926 (November 2007) Impaired tRNA Nuclear Export Links DNA Damage and Cell-Cycle Checkpoint  Ata Ghavidel, Thomas Kislinger, Oxana Pogoutse, Richelle Sopko, Igor Jurisica, Andrew Emili  Cell  Volume 131, Issue 5, Pages 915-926 (November 2007) DOI: 10.1016/j.cell.2007.09.042 Copyright © 2007 Elsevier Inc. Terms and Conditions

Figure 1 DNA Damage Induces Downregulation of tRNA Splicing (A) A simplified schematic representation of tRNA primary transcript processing. (B) Defective tRNA intron excision in log-phase cultures of S288C wild-type yeast in rich media (YPD) after MMS treatment (0.04% v/v) for 80 min. Northern blot of the tRNAIle transcript with probes, denoted by short, thick lines, complementary to 5′ and 3′ splice junctions or to the intron itself. Primary precursor and end-processed, unspliced transcripts are depicted. (C) Time course analysis of splicing of the indicated tRNA species after UV irradiation (60 J/m2). (D) Quantification of tRNAIle and tRNALeu splicing efficiency after UV exposure. Data were normalized to untreated controls (not shown); bars indicate standard deviation across three independent experiments. Cell 2007 131, 915-926DOI: (10.1016/j.cell.2007.09.042) Copyright © 2007 Elsevier Inc. Terms and Conditions

Figure 2 Downregulation of tRNA Splicing Requires an Intact Signaling Pathway (A) Induction of DNA double-strand breaks perturbs tRNA splicing. (Top) Genomic DNA from S288C wild-type cells harboring a galactose-inducible pGal-EcoRI, expressing the endonuclease EcoRI, grown in glucose or galactose, and stained with ethidium bromide. (Bottom) tRNAIle splicing, with a probe complementary to its intron, in cells harboring control (pGal) or pGal-EcoRI. Ratio of end-processed to primary unspliced tRNAIle is denoted; control is assigned an arbitrary value of 1. (B) MMS (0.04%) reduces tRNAIle splicing in α-factor-arrested cells. Quantification as in (A). (C) tRNAIle splicing in select checkpoint mutants exposed to MMS (0.04%) for 80 min. Cell 2007 131, 915-926DOI: (10.1016/j.cell.2007.09.042) Copyright © 2007 Elsevier Inc. Terms and Conditions

Figure 3 Induction of DNA Damage Specifically Attenuates Nuclear Export of Intron-Containing tRNA (A) MMS-induced nuclear retention of precursor tRNA. Log-phase wild-type cells were treated with 0.04% MMS for 80 min. The subcellular distribution of intron-containing tRNAIleUAU transcripts was monitored in situ by fluorescence microscopy (FITC) by using a DIG-labeled oligo complementary to its intron. The nuclei were counterstained with DAPI. (B) Quantification of the nucleocytoplasmic distribution of tRNAIleUAU. The subcellular abundance of the tRNAIle transcript in a population of cells was determined by quantifying the FITC signal intensity in the nuclear and cytoplasmic compartments (grouped into bins on the x axis). The number of cells in each bin, as a percentage of the total cell population assayed, is plotted on the y axis. (C) The subcellular distribution of intron-containing tRNAIleUAU in a rad53Δ mutant. (D) Quantification of (C). Cell 2007 131, 915-926DOI: (10.1016/j.cell.2007.09.042) Copyright © 2007 Elsevier Inc. Terms and Conditions

Figure 4 MMS Treatment Results in Subcellular Redistribution of tRNA Export Factor Los1 (A) In vivo tRNAIleUAU splicing in wild-type and los1Δ cells harvested 30 min after UV irradiation (60 J/m2) or 80 min after MMS (0.04%) treatment. Total RNA was assayed with an oligo complementary to the tRNAIle intron. (B) Subcellular distribution of intron-containing tRNAIleUAU in a los1 mutant in situ by fluorescence microscopy as in Figure 3A. (C) Quantification of the nucleocytoplasmic distribution of tRNAIleUAU as in Figure 3B. (D) Los1-TAP abundance monitored by western blot of whole-cell lysates from untreated and MMS-treated cells. The mitochondrial porin served as the loading control. (E) In situ localization of Los1-GFP in wild-type and rad53Δ cells before or after MMS exposure (0.04% for 80 min). Successive images for GFP and DAPI are shown. (F) Differential recovery of Los1-TAP in cytoplasmic fractions after MMS treatment determined by western blot of the cytosolic fractions and lysates from Ficol-gradient-purified nuclei. The canonical TATA-box binding protein (TBP) served as a nuclear marker. (G) In situ localization of C-terminally GFP-tagged Kap111, Kap122, and Rna1 before and after MMS treatment. Cell 2007 131, 915-926DOI: (10.1016/j.cell.2007.09.042) Copyright © 2007 Elsevier Inc. Terms and Conditions

Figure 5 Deletion of LOS1 Restores G1 Arrest and Enhances Viability in a rad53 Mutant in Response to DNA Damage (A) tRNAIleUAU splicing in wild-type, los1Δ, rad53Δ, and rad53Δ los1Δ mutants assayed by northern blot with an oligo complementary to its intron. The ratio of end-processed to primary unspliced tRNAIle is denoted; untreated wild-type cells are assigned an arbitrary value of 1. (B) Delayed G1 progression in rad53Δ mutants by deleting LOS1. Logarithmically growing (log) cells were arrested in G1 by α-factor and were treated with MMS or left untreated. These cells were subsequently released into fresh media and analyzed by FACS. (C) Reduction in MMS hypersensitivity of rad53Δ mutants by deleting LOS1. After MMS treatment, viability was determined by counting colonies after a 3 day incubation at 30°C. Cell 2007 131, 915-926DOI: (10.1016/j.cell.2007.09.042) Copyright © 2007 Elsevier Inc. Terms and Conditions

Figure 6 Impaired tRNA Export Contributes to G1 Checkpoint by Delaying Accumulation of Cln2 (A) Time course analysis of Cln2-TAP accumulation during cell-cycle recovery of wild-type cells after synchronization with α-factor, with or without exposure to MMS. Porin served as a loading control. (B) Cln2-TAP and Porin mRNA levels prepared from cells in (A). (C) Quantification of Cln2-TAP protein, normalized to its cognate mRNA, in unperturbed or MMS-treated cells as depicted in (A) and (B) (see text for detail). (D) Cln2-TAP protein levels in control and MMS-treated rad53Δ or rad53Δ los1Δ mutants. (E) Quantification of Cln2-TAP protein levels depicted in (D). Cell 2007 131, 915-926DOI: (10.1016/j.cell.2007.09.042) Copyright © 2007 Elsevier Inc. Terms and Conditions

Figure 7 Impaired tRNA Export Signals MMS-Induced G1 Arrest by Activating Gcn4 (A) β-galactosidase activity in strains that harbor a GCN4-lacZ reporter plasmid. Logarithmically growing cells, grown in Ura– media, were treated with 0.04% MMS for 80 min prior to being processed for β-galactosidase activity, denoted on the x axis (Miller units∗10−1). (B and C) (B) Time course analysis of Cln2-TAP accumulation during recovery of a wild-type and an isogenic gcn4Δ strain after synchronization with α-factor, with or without exposure to MMS. Porin served as a loading control for quantification in (C). (D) Cell-cycle progression in MMS-treated gcn4Δ mutants. Logarithmically growing cells were synchronized in G1 by α-factor and were treated with MMS or left untreated. These cells were subsequently released into fresh media, and their progression through the cell cycle was monitored at the indicated time points by FACS. (E) A working model for regulated nucleocytoplasmic trafficking of tRNA after DNA damage. In cells with DNA damage, a Mec1/Rad53-dependent signaling pathway, via yet to be identified downstream effector(s), impinges on the export process via differential relocalization of Los1 to the cytoplasm. The ensuing nuclear accumulation of tRNA signals activation of Gcn4, which, in turn, contributes to the execution of the G1 checkpoint by delaying the accumulation of cyclin Cln2, and likely other key regulators of G1 progression. Cell 2007 131, 915-926DOI: (10.1016/j.cell.2007.09.042) Copyright © 2007 Elsevier Inc. Terms and Conditions